Multi-agents systems and holonic manufacturing systems are suitable approaches to design a new and alternative class of production control systems, based on the decentralization of control functions over distributed autonomous and cooperative entities. However, in spite of their enormous potential they lack some aspects related to interoperability, migration, optimisation in decentralised structures and truly self-adaptation. This paper discusses the advantages of combining these paradigms with complementary paradigms, such as service-oriented architectures, and enhancing them with biologically inspired algorithms and techniques, such as emergent behaviour and self-organization, to reach a truly robust, agile and adaptive control system. An example of applying a stigmergy-based algorithm to dynamically route pallets in a production system is also provided.